A decadal view of biodiversity informatics: challenges and priorities

Biodiversity informatics plays a central enabling role in the research community's efforts to address scientific conservation and sustainability issues. Great strides have been made in the past decade establishing a framework for sharing data, where taxonomy and systematics has been perceived as the most prominent discipline involved. To some extent this is inevitable, given the use of species names as the pivot around which information is organised. To address the urgent questions around conservation, land-use, environmental change, sustainability, food security and ecosystem services that are facing Governments worldwide, we need to understand how the ecosystem works. So, we need a systems approach to understanding biodiversity that moves significantly beyond taxonomy and species observations. Such an approach needs to look at the whole system to address species interactions, both with their environment and with other species. It is clear that some barriers to progress are sociological, basically persuading people to use the technological solutions that are already available. This is best addressed by developing more effective systems that deliver immediate benefit to the user, hiding the majority of the technology behind simple user interfaces. An infrastructure should be a space in which activities take place and, as such, should be effectively invisible. This community consultation paper positions the role of biodiversity informatics, for the next decade, presenting the actions needed to link the various biodiversity infrastructures invisibly and to facilitate understanding that can support both business and policy-makers. The community considers the goal in biodiversity informatics to be full integration of the biodiversity research community, including citizens’ science, through a commonly-shared, sustainable e-infrastructure across all sub-disciplines that reliably serves science and society alike

Quantifying Vegetation Biophysical Variables from Imaging Spectroscopy Data: A Review on Retrieval Methods

An unprecedented spectroscopic data stream will soon become available with forthcoming Earth-observing satellite missions equipped with imaging spectroradiometers. This data stream will open up a vast array of opportunities to quantify a diversity of biochemical and structural vegetation properties. The processing requirements for such large data streams require reliable retrieval techniques enabling the spatiotemporally explicit quantification of biophysical variables. With the aim of preparing for this new era of Earth observation, this review summarizes the state-of-the-art retrieval methods that have been applied in experimental imaging spectroscopy studies inferring all kinds of vegetation biophysical variables. Identified retrieval methods are categorized into: (1) parametric regression, including vegetation indices, shape indices and spectral transformations; (2) nonparametric regression, including linear and nonlinear machine learning regression algorithms; (3) physically based, including inversion of radiative transfer models (RTMs) using numerical optimization and look-up table approaches; and (4) hybrid regression methods, which combine RTM simulations with machine learning regression methods. For each of these categories, an overview of widely applied methods with application to mapping vegetation properties is given. In view of processing imaging spectroscopy data, a critical aspect involves the challenge of dealing with spectral multicollinearity. The ability to provide robust estimates, retrieval uncertainties and acceptable retrieval processing speed are other important aspects in view of operational processing. Recommendations towards new-generation spectroscopy-based processing chains for operational production of biophysical variables are given

Metabolic rates at different oxygen levels determined by direct and indirect calorimetry in the oxyconformer Sipunculus nudus

Oxygen uptake and the mode of energy production in Sipunculus nudus L. were determined at different oxygen levels by means of direct and indirect calorimetry. Oxygen consumption declined linearly with decreasing ambient POr A similar decrease in heat production was observed down to a Po2 of 8.66 kPa. At lower oxygen tensions, a discrepancy between aerobic and total heat production indicated the onset of anaerobic metabolism. The occurrence of the critical POl between 8.66 and 2.66 kPa was confirmed by estimation of anaerobic end products in the body wall musculature. The contributions of aerobic and anaerobic metabolism to total ATP production were determined at a Po2 of 2.66 kPa and were found to be 48 and 52 %, respectively. Measured heat dissipation under extreme hypoxia (Po2 nominally zero) (21.5±3.5mJh ~ 1 g ~ 1) agreed with the enthalpy changes calculated from the rates of formation of anaerobic end products (17.9±4.7mJh ~ 1 g ~ 1). For the sake of redox balance maintenance, saturation of fatty acids was assumed; this would be accompanied by an additional heat production of 3.3mJh^'g " 1, so that the total calculated enthalpy change 1 1 amounted to 21

Detecting soil water use by Mediterranean vegetation on rocky soils using electrical resistivity tomography.

Water availability is an important constraint on tree and shrub development in Mediterranean ecosystems. During prolonged periods of summer drought, water stored in the soil column is the only available water source. Some Mediterranean tree species are known to have extensive root system penetrating deeply into fractured bedrock. Accurate characterisation of the soil and the ability of trees to subtract water from the soil profile are crucial for the understanding of Mediterranean ecosystems and the modelling of primary production. However, with shallow soils on rocky substrate, it is hard to obtain soil moisture data at depths below 30-50 cm. We explored the use of Electrical Resistivity Tomography (ERT) to detect vegetation water use trough the whole soil column. ERT provides spatial information on soil conditions and moisture content down to 5 m and deeper in a 2D cross-section. It uses a multi-electrode array that is connected to the soil through steel pins that are inserted in the ground. This method of installation allows measurements on rocky substrate. We used ERT to detect spatial and temporal patterns of soil moisture in variable shallow soils and weathered bedrock of the Peyne area in Mediterranean southern France. The Peyne area has a sub-humid climate and is covered mainly in sclerophyllous trees and shrubs. ERT measurements were made for 13 sites in the study area which were all visited in June, at the onset of the dry season, and again in September, near the end of a three-month dry period. Our measurements show root penetration and water use by trees 5m and deeper, despite the shallow soils in the study area. We also show large short-scale spatial variability and the importance of the geological substrate in moisture processes. ERT is a useful new technique for the exploration of soil and ecosystem functioning, even with rocky soils, providing information on rooting depth and water use otherwise unavailable